Genetically-based sperm discrimination in the vaginal tract of a primate species

Females influence offspring paternity through diverse pre- and post-copulatory mechanisms. Sperm discrimination within the reproductive tract of females is observed in insects, birds, and rodents, but current evidence among large-bodied mammals is absent. Here, we tested whether two aspects of female physiology that affect sperm survival- vaginal immune response and pH- are modulated by male genetic makeup in a nonhuman primate. This dataset includes 3 files: 1. anubis_featurecounts.Rdata : Gene count matrix created from whole transcriptome sequencing of 106 vaginal swabs and 8 semen samples. We generated RNA sequencing libraries using strand-specific library preparation with the NEBNext Ultra II RNA kit with rRNA depletion and sequenced on one NovaSeq6000 S2 100 cycle v1.5 run, generating 50 bp PE reads. We processed the raw sequencing data using the RNAseq_data_processing.sh file available at www.github.com/rachpetersen/cryptic_choice_anubis. 2. DE_sample_metadata.csv : Metadata for vaginal RNA-seq samples including 10 metrics of male genetic dviersity and mating dyad complementarity. Genotyping methods are described in detail in Petersen, R. M., Bergey, C. M., Roos, C., & Higham, J. P. (2022). Relationship between genome‐wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate. Ecology and Evolution, 12(10), e9346. 3. pH_data.csv : Vaginal pH measurements with modeling metadata including male genetic diversity and genetic complementarity of the mating dyad.雌性通过多样的交配前与交配后机制（pre- and post-copulatory mechanisms）影响后代父权（paternity）。在昆虫、鸟类与啮齿类动物中已观测到雌性生殖道（reproductive tract）内的精子甄别（sperm discrimination）现象，但目前针对大型哺乳动物的相关证据仍付阙如。本研究以非人灵长类为研究对象，检验了两项影响精子存活的雌性生理特征——阴道免疫应答（vaginal immune response）与pH值——是否受雄性遗传背景的调控。 本数据集包含3个文件： 1. anubis_featurecounts.Rdata：该文件为基因计数矩阵，由106份阴道拭子与8份精液样本的全转录组测序（whole transcriptome sequencing）数据构建。我们采用搭载rRNA去除（rRNA depletion）步骤的NEBNext Ultra II RNA试剂盒完成链特异性文库制备（strand-specific library preparation），并在NovaSeq6000 S2 100循环v1.5测序平台上完成测序，生成50 bp双端读段（PE reads）。原始测序数据的处理流程可通过公开脚本RNAseq_data_processing.sh实现，脚本获取地址为www.github.com/rachpetersen/cryptic_choice_anubis。 2. DE_sample_metadata.csv：该文件为阴道RNA测序样本的元数据（metadata），包含10项雄性遗传多样性（genetic diversity）指标以及交配二元组（mating dyad）的遗传互补性（genetic complementarity）信息。基因分型（genotyping）方法的详细描述参见以下文献：Petersen, R. M., Bergey, C. M., Roos, C., & Higham, J. P. (2022). 非人灵长类动物全基因组与主要组织相容性复合体（Major Histocompatibility Complex，MHC）I类、II类的遗传多样性及互补性关系. Ecology and Evolution, 12(10), e9346。 3. pH_data.csv：该文件包含阴道pH测量数据以及配套建模元数据，其中涵盖雄性遗传多样性与交配二元组的遗传互补性信息。